[yt-users] Fwd: install failure

Mordecai-Mark Mac Low mordecai at amnh.org
Sun Sep 28 18:57:04 PDT 2014


Here’s are examples of the problem. yt fails immediately with any usage. As you can see, I don’t have a lot of information here!


[yt-x86_64] sagittariusb 1 % yt
Abort
[yt-x86_64] sagittariusb 2 % yt --help
Abort
[yt-x86_64] sagittariusb 3 % python
Python 2.7.8 (default, Sep 28 2014, 20:55:56) 
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.51)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import yt
Abort
[yt-x86_64] sagittariusb 4 % 

I tried your suggestion of using the bash activate script:

[yt-x86_64] sagittariusB 40 % bash yt-x86_64/bin/activate
[yt-x86_64] sagittariusB 41 % yt
Abort
[yt-x86_64] sagittariusB 42 % 


FWIW, I do note that the “Abort” appears to be appearing a lot faster with the readline problem corrected.

- Mordecai


Begin forwarded message:

> From: Nathan Goldbaum <nathan12343 at gmail.com>
> Subject: Re: [yt-users] install failure
> Date: September 28, 2014 at 21:38:36 EDT
> To: Mordecai-Mark Mac Low <mordecai at amnh.org>
> Cc: <teuben at astro.umd.edu>
> 
> 
> In your original message you said that you were using activate.csh - can you under bash with the bash activate script?
> 
> When you say "on startup", can you copy/paste a session where the error happens?  Are you saying that python is failing to start or do you get the abort error when you import yt?
> 
> On Sun, Sep 28, 2014 at 6:35 PM, Mordecai-Mark Mac Low <mordecai at amnh.org> wrote:
> I’m taking this off the general list for the moment…
> 
> I have replaced readline with gnureadline as you suggested, and that does eliminate the error during installation (see https://dl.dropboxusercontent.com/u/31830722/yt_install-v2.log).  Unfortunately, it doesn’t change the behavior on startup: Abort, with no further errors.
> 
> At Peter Teuben’s suggestion, I also ran dtruss on this, but he saw nothing obviously wrong — just a whole lot of files being opened (around 900 at his estimate).
> 
> - Mordecai
> 
>  
> On Sep 28, 2014, at 20:45, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
> 
>> 
>> ---------- Forwarded message ----------
>> From: Nathan Goldbaum <nathan12343 at gmail.com>
>> Date: Sun, Sep 28, 2014 at 5:29 PM
>> Subject: Re: [yt-users] install failure
>> To: Discussion of the yt analysis package <yt-users at lists.spacepope.org>
>> 
>> 
>> So looking at the install log, it's actually the install script that's trying to build readline, right here: https://bitbucket.org/yt_analysis/yt/src/4cf5c5369df9b012759ab979330d8e356d1b0e00/doc/install_script.sh?at=yt#cl-987
>> 
>> I'm actually able to reproduce this on my OSX Mavericks laptop when I do "pip install readline".  It seems that the readline package on pypi hasn't been updated since 2012: https://pypi.python.org/pypi/readline.  
>> 
>> I never noticed this issue because I use homebrew's python, and homebrew links against the gnu readline library when they build python.
>> 
>> It seems the gnureadline package has supplanted the old readline package: https://pypi.python.org/pypi/gnureadline
>> 
>> I've gone ahead and created a pull request to make the install script install gnureadline instead of readline: https://bitbucket.org/yt_analysis/yt/pull-request/1225/install-gnureadline-package-since-readline/diff
>> 
>> You can probably just modify your local copy of the install script to use "pip install gnureadline" instead of "pip install readline".
>> 
>> Hope that fixes your issue, thanks very much for the report.
>> 
>> -Nathan
>> 
>> On Sun, Sep 28, 2014 at 5:00 PM, Mordecai-Mark Mac Low <mordecai at amnh.org> wrote:
>> Nathan,
>> 
>> I’ve posted the full install log to
>> 
>> https://dl.dropboxusercontent.com/u/31830722/yt_install.log
>> 
>> It does look like ipython is trying to compile readline.
>> 
>> I have the regular Mac Python installation, but would have to learn anaconda or canopy before using them for an installation, which I was hoping to avoid for the moment by using the install script.
>> 
>> Best,
>> 
>> Mordecai
>> 
>> 
>> On Sep 28, 2014, at 19:33, yt-users-request at lists.spacepope.org wrote:
>> > Message: 1
>> > Date: Sun, 28 Sep 2014 13:57:47 -0700
>> > From: Nathan Goldbaum <nathan12343 at gmail.com>
>> > To: Discussion of the yt analysis package
>> >       <yt-users at lists.spacepope.org>
>> > Subject: Re: [yt-users] install failure
>> > Message-ID:
>> >       <CAJXewO=G9M7V0deBGtU46s68kdKPVTqsmhEBxV+yG7-K=8HcgQ at mail.gmail.com>
>> > Content-Type: text/plain; charset="utf-8"
>> >
>> > Hi Mordecai,
>> >
>> > We've had some reports about incompatibilities with the install script on
>> > OS X Mavericks recently, but I don't think this error has been reported
>> > before. Unfortunately getting the install script to work portably in all
>> > cases is a labor of love and sometimes errors like these crop up.
>> >
>> > Googling for your error returns this discussion on the readline mailing
>> > list: https://lists.gnu.org/archive/html/bug-readline/2013-12/msg00002.html.
>> > Apparently the version you're compiling needs to be patched to compile
>> > cleanly on mavericks.  I haven't checked whether the patch has made its way
>> > into a readline release.
>> >
>> > I'm not sure what exactly is compiling readline (IPython maybe?), but
>> > earlier in the install script we should have installed a pure-python
>> > version of the readline library from pypi if we were unable to import it.
>> > It would help to figure out what went wrong if you could upload the full
>> > install log somewhere.
>> >
>> > Do you have a python environment setup on your laptop already?  It's very
>> > straightforward to install yt using anaconda, canopy, or a manually
>> > configured python environment, bypassing all the bootstrapping that the
>> > install script must do.  Take a look at the following page in the
>> > documentation:
>> >
>> > http://yt-project.org/doc/installing.html#installing-yt-using-anaconda
>> > http://yt-project.org/doc/installing.html#installing-yt-using-pip-or-from-source
>> >
>> > Hope that's helpful.
>> >
>> > -Nathan
>> >
>> >
>> > On Sun, Sep 28, 2014 at 12:36 PM, Mordecai-Mark Mac Low <mordecai at amnh.org>
>> > wrote:
>> >
>> >> Hi, I am having a fatal problem installing yt on my MacBook Pro running OS
>> >> X v10.9.4.  I am using the install script, with the options set as follows:
>> >>
>> >>
>> >> # Here's where you put the HDF5 path if you like; otherwise it'll download
>> >> it
>> >> # and install it on its own
>> >> #HDF5_DIR=/opt/local/lib
>> >>
>> >> # If you need to supply arguments to the NumPy or SciPy build, supply them
>> >> here
>> >> # This one turns on gfortran manually:
>> >> #NUMPY_ARGS="--fcompiler=gnu95"
>> >> # If you absolutely can't get the fortran to work, try this:
>> >> #NUMPY_ARGS="--fcompiler=fake"
>> >>
>> >> INST_HG=0       # Install Mercurial or not?  If hg is not already
>> >>                # installed, yt cannot be installed.
>> >> INST_ZLIB=1     # On some systems (Kraken) matplotlib has issues with
>> >>                # the system zlib, which is compiled statically.
>> >>                # If need be, you can turn this off.
>> >> INST_BZLIB=1    # On some systems, libbzip2 is missing.  This can
>> >>                # lead to broken mercurial installations.
>> >> INST_PNG=1      # Install a local libpng?  Same things apply as with zlib.
>> >> INST_FTYPE=1    # Install FreeType2 locally?
>> >> INST_ENZO=0     # Clone a copy of Enzo?
>> >> INST_SQLITE3=1  # Install a local version of SQLite3?
>> >> INST_PYX=1      # Install PyX?  Sometimes PyX can be problematic without a
>> >>                # working TeX installation.
>> >> INST_0MQ=1      # Install 0mq (for IPython) and affiliated bindings?
>> >> INST_ROCKSTAR=1 # Install the Rockstar halo finder?
>> >> INST_SCIPY=0    # Install scipy?
>> >>
>> >>
>> >> After downloading and activating Xcode command line tools, I got the
>> >> script to complete successfully. I activated it using the activate.csh
>> >> script.
>> >>
>> >> However, when I then try to start yt, it pauses for 30 seconds or so, and
>> >> then issues the response ?Abort?, with no further errors.  I get the same
>> >> response if I try to import yt into the python (running in the yt
>> >> environment). Abort, and return to the command line.
>> >>
>> >> I have tried erasing the yt-x86_64 directory and reinstalling from
>> >> scratch, with no change in behavior.  I also examined the yt_install.log.
>> >> I found a number of, presumably irrelevant, errors in the configuration
>> >> tests, but also an error at the end of the long section on building Ipython
>> >> (almost at the end of the script, just before readline assembly that looks
>> >> possibly relevant:
>> >>
>> >>    gcc -dynamic -arch i386 -arch x86_64 -arch_only `/usr/bin/arch`
>> >> -install_name /usr/local/lib/libreadline.6.2.dylib -current_version 6.2
>> >> -compatibility_version 6 -v -o libreadline.6.2.dylib readline.so vi_mode.so
>> >> funmap.so keymaps.so parens.so search.so rltty.so complete.so bind.so
>> >> isearch.so display.so signals.so util.so kill.so undo.so macro.so input.so
>> >> callback.so terminal.so text.so nls.so misc.so xmalloc.so xfree.so
>> >> history.so histexpand.so histfile.so histsearch.so shell.so mbutil.so
>> >> tilde.so compat.so -lncurses
>> >>    Apple LLVM version 6.0 (clang-600.0.51) (based on LLVM 3.5svn)
>> >>    Target: x86_64-apple-darwin13.3.0
>> >>    Thread model: posix
>> >>    clang: error: invalid argument '-compatibility_version 6' only allowed
>> >> with '-dynamiclib'
>> >>    clang: error: invalid argument '-compatibility_version 6' only allowed
>> >> with '-dynamiclib'
>> >>    make[1]: *** [libreadline.6.2.dylib] Error 1
>> >>    make: [shared] Error 2 (ignored)
>> >>
>> >> Any insight on how to proceed?
>> >>
>> >> Best,
>> >>
>> >> Mordecai
>> >>
>> >>
>> >> --
>> >> Mordecai-Mark Mac Low  Curator & Professor
>> >> +1-212-496-3443          Department of Astrophysics
>> >> +1-212-769-5007 (fax)    American Museum of Natural History
>> >> mmaclow (Skype, Hangout)     79th St at CPW, NY, NY, 10024-5192, USA
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> _______________________________________________
>> >> yt-users mailing list
>> >> yt-users at lists.spacepope.org
>> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >>
>> >>
>> > -------------- next part --------------
>> > An HTML attachment was scrubbed...
>> > URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20140928/d7562d47/attachment.htm>
>> >
>> > ------------------------------
>> >
>> > Message: 2
>> > Date: Sun, 28 Sep 2014 19:33:51 -0400
>> > From: Professor Maller <amaller at citytech.cuny.edu>
>> > To: yt-users at lists.spacepope.org
>> > Subject: Re: [yt-users] install failure
>> > Message-ID:
>> >       <CACCSjdNPC0QVrxDooBEQ2W7Mp6KaBJxNJZ9eLvH6TG8WyD7m0Q at mail.gmail.com>
>> > Content-Type: text/plain; charset="utf-8"
>> >
>> > Hi Mordecai,
>> >
>> > Depending on what you want to do with yt, if you need the latest build or
>> > not, but I've had success on Mac with the anaconda distribution of python
>> > which includes yt-3.0. https://store.continuum.io/cshop/anaconda/.
>> >
>> >
>> > Ari
>> >
>> >
>> >
>> > On Sun, Sep 28, 2014 at 4:30 PM, <yt-users-request at lists.spacepope.org>
>> > wrote:
>> >
>> >> Send yt-users mailing list submissions to
>> >>        yt-users at lists.spacepope.org
>> >>
>> >> To subscribe or unsubscribe via the World Wide Web, visit
>> >>        http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >> or, via email, send a message with subject or body 'help' to
>> >>        yt-users-request at lists.spacepope.org
>> >>
>> >> You can reach the person managing the list at
>> >>        yt-users-owner at lists.spacepope.org
>> >>
>> >> When replying, please edit your Subject line so it is more specific
>> >> than "Re: Contents of yt-users digest..."
>> >>
>> >>
>> >> Today's Topics:
>> >>
>> >>   1. Re: ProfilePlot in YT-3.0 (Nathan Goldbaum)
>> >>   2. install failure (Mordecai-Mark Mac Low)
>> >>   3. Re: install failure (Peter Teuben)
>> >>
>> >>
>> >> ----------------------------------------------------------------------
>> >>
>> >> Message: 1
>> >> Date: Sun, 28 Sep 2014 12:14:04 -0700
>> >> From: Nathan Goldbaum <nathan12343 at gmail.com>
>> >> To: Discussion of the yt analysis package
>> >>        <yt-users at lists.spacepope.org>
>> >> Subject: Re: [yt-users] ProfilePlot in YT-3.0
>> >> Message-ID:
>> >>        <
>> >> CAJXewOkKaMPBE02RH_VY4rNTXgOobeJ02qOOZY5PRk332GGveg at mail.gmail.com>
>> >> Content-Type: text/plain; charset="utf-8"
>> >>
>> >> On Sunday, September 28, 2014, John Regan <johnanthonyregan at gmail.com>
>> >> wrote:
>> >>
>> >>> Hi Nathan,
>> >>>
>> >>> Thanks for that. I'll have a look at what helper functions would be
>> >> useful
>> >>> as I use the ProfilePlot routine and I can issue a PR then. I think it
>> >>> would be worth updating the docs with info like you just sent me.
>> >>>
>> >>
>> >> Again, please feel free to open a pull request.
>> >>
>> >>
>> >>>
>> >>> Cheers,
>> >>> John
>> >>>
>> >>> On Sun, Sep 28, 2014 at 11:17 AM, Nathan Goldbaum <nathan12343 at gmail.com
>> >>> <javascript:_e(%7B%7D,'cvml','nathan12343 at gmail.com');>> wrote:
>> >>>
>> >>>> Hi John,
>> >>>>
>> >>>> ProfilePlot is a wrapper around the Profile1D class, which calculates
>> >> and
>> >>>> stores the histograms.  To access the underlying data you need to access
>> >>>> the profile object via the profiles attribute of the ProfilePlot:
>> >>>>
>> >>>> import yt
>> >>>> ds = yt.load('IsolatedGalaxy/galaxy0030/galaxy0030')
>> >>>> plot = yt.ProfilePlot(ds.all_data(), 'radius', 'density')
>> >>>> profile = plot.profiles[0]
>> >>>> print profile.x_field, profile.x
>> >>>> print profile.field_data.keys(), profile['density']
>> >>>>
>> >>>> There are probably a number of ways that the current API can be improved
>> >>>> to make it more straightforward to access this data.  PRs along this
>> >> front
>> >>>> would be very welcome, I think.
>> >>>>
>> >>>> -Nathan
>> >>>>
>> >>>> On Sun, Sep 28, 2014 at 1:05 AM, John Regan <johnanthonyregan at gmail.com
>> >>>> <javascript:_e(%7B%7D,'cvml','johnanthonyregan at gmail.com');>> wrote:
>> >>>>
>> >>>>> HI All,
>> >>>>>
>> >>>>> Is there an easy way to access the x_field and the y_fields in the
>> >>>>> ProfilePlot function?
>> >>>>>
>> >>>>> So for example
>> >>>>>
>> >>>>> prof = ProfilePlot(sphere, "radius", "density")
>> >>>>>
>> >>>>>
>> >>>>> print prof.x_field
>> >>>>> print prof.y_field[0]
>> >>>>>
>> >>>>> I inserted a couple of hack functions into the ProfilePlot class to
>> >>>>> return the x_field and the .items() tuple but there is probably a
>> >> better
>> >>>>> way?
>> >>>>>
>> >>>>> John
>> >>>>>
>> >>>>> _______________________________________________
>> >>>>> yt-users mailing list
>> >>>>> yt-users at lists.spacepope.org
>> >>>>> <javascript:_e(%7B%7D,'cvml','yt-users at lists.spacepope.org');>
>> >>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >>>>>
>> >>>>>
>> >>>>
>> >>>> _______________________________________________
>> >>>> yt-users mailing list
>> >>>> yt-users at lists.spacepope.org
>> >>>> <javascript:_e(%7B%7D,'cvml','yt-users at lists.spacepope.org');>
>> >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >>>>
>> >>>>
>> >>>
>> >> -------------- next part --------------
>> >> An HTML attachment was scrubbed...
>> >> URL: <
>> >> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20140928/2844d4aa/attachment.htm
>> >>>
>> >>
>> >> ------------------------------
>> >>
>> >> Message: 2
>> >> Date: Sun, 28 Sep 2014 15:36:55 -0400
>> >> From: Mordecai-Mark Mac Low <mordecai at amnh.org>
>> >> To: <yt-users at lists.spacepope.org>
>> >> Subject: [yt-users] install failure
>> >> Message-ID: <C2FC80DA-9E95-476E-BB68-E5944D4597F3 at amnh.org>
>> >> Content-Type: text/plain; charset="windows-1252"
>> >>
>> >> Hi, I am having a fatal problem installing yt on my MacBook Pro running OS
>> >> X v10.9.4.  I am using the install script, with the options set as follows:
>> >>
>> >>
>> >> # Here's where you put the HDF5 path if you like; otherwise it'll download
>> >> it
>> >> # and install it on its own
>> >> #HDF5_DIR=/opt/local/lib
>> >>
>> >> # If you need to supply arguments to the NumPy or SciPy build, supply them
>> >> here
>> >> # This one turns on gfortran manually:
>> >> #NUMPY_ARGS="--fcompiler=gnu95"
>> >> # If you absolutely can't get the fortran to work, try this:
>> >> #NUMPY_ARGS="--fcompiler=fake"
>> >>
>> >> INST_HG=0       # Install Mercurial or not?  If hg is not already
>> >>                # installed, yt cannot be installed.
>> >> INST_ZLIB=1     # On some systems (Kraken) matplotlib has issues with
>> >>                # the system zlib, which is compiled statically.
>> >>                # If need be, you can turn this off.
>> >> INST_BZLIB=1    # On some systems, libbzip2 is missing.  This can
>> >>                # lead to broken mercurial installations.
>> >> INST_PNG=1      # Install a local libpng?  Same things apply as with zlib.
>> >> INST_FTYPE=1    # Install FreeType2 locally?
>> >> INST_ENZO=0     # Clone a copy of Enzo?
>> >> INST_SQLITE3=1  # Install a local version of SQLite3?
>> >> INST_PYX=1      # Install PyX?  Sometimes PyX can be problematic without a
>> >>                # working TeX installation.
>> >> INST_0MQ=1      # Install 0mq (for IPython) and affiliated bindings?
>> >> INST_ROCKSTAR=1 # Install the Rockstar halo finder?
>> >> INST_SCIPY=0    # Install scipy?
>> >>
>> >>
>> >> After downloading and activating Xcode command line tools, I got the
>> >> script to complete successfully. I activated it using the activate.csh
>> >> script.
>> >>
>> >> However, when I then try to start yt, it pauses for 30 seconds or so, and
>> >> then issues the response ?Abort?, with no further errors.  I get the same
>> >> response if I try to import yt into the python (running in the yt
>> >> environment). Abort, and return to the command line.
>> >>
>> >> I have tried erasing the yt-x86_64 directory and reinstalling from
>> >> scratch, with no change in behavior.  I also examined the yt_install.log.
>> >> I found a number of, presumably irrelevant, errors in the configuration
>> >> tests, but also an error at the end of the long section on building Ipython
>> >> (almost at the end of the script, just before readline assembly that looks
>> >> possibly relevant:
>> >>
>> >>    gcc -dynamic -arch i386 -arch x86_64 -arch_only `/usr/bin/arch`
>> >> -install_name /usr/local/lib/libreadline.6.2.dylib -current_version 6.2
>> >> -compatibility_version 6 -v -o libreadline.6.2.dylib readline.so vi_mode.so
>> >> funmap.so keymaps.so parens.so search.so rltty.so complete.so bind.so
>> >> isearch.so display.so signals.so util.so kill.so undo.so macro.so input.so
>> >> callback.so terminal.so text.so nls.so misc.so xmalloc.so xfree.so
>> >> history.so histexpand.so histfile.so histsearch.so shell.so mbutil.so
>> >> tilde.so compat.so -lncurses
>> >>    Apple LLVM version 6.0 (clang-600.0.51) (based on LLVM 3.5svn)
>> >>    Target: x86_64-apple-darwin13.3.0
>> >>    Thread model: posix
>> >>    clang: error: invalid argument '-compatibility_version 6' only allowed
>> >> with '-dynamiclib'
>> >>    clang: error: invalid argument '-compatibility_version 6' only allowed
>> >> with '-dynamiclib'
>> >>    make[1]: *** [libreadline.6.2.dylib] Error 1
>> >>    make: [shared] Error 2 (ignored)
>> >>
>> >> Any insight on how to proceed?
>> >>
>> >> Best,
>> >>
>> >> Mordecai
>> >>
>> >>
>> >> --
>> >> Mordecai-Mark Mac Low           Curator & Professor
>> >> +1-212-496-3443                 Department of Astrophysics
>> >> +1-212-769-5007 (fax)           American Museum of Natural History
>> >> mmaclow (Skype, Hangout)        79th St at CPW, NY, NY, 10024-5192, USA
>> >>
>> >>
>> >>
>> >>
>> >> -------------- next part --------------
>> >> An HTML attachment was scrubbed...
>> >> URL: <
>> >> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20140928/28fdb738/attachment.htm
>> >>>
>> >>
>> >> ------------------------------
>> >>
>> >> Message: 3
>> >> Date: Sun, 28 Sep 2014 16:30:01 -0400
>> >> From: Peter Teuben <teuben at astro.umd.edu>
>> >> To: yt-users at lists.spacepope.org
>> >> Subject: Re: [yt-users] install failure
>> >> Message-ID: <54286FC9.1010003 at astro.umd.edu>
>> >> Content-Type: text/plain; charset="windows-1252"
>> >>
>> >>
>> >> just "abort" usually tells me it can't find enough memory while loading
>> >> the executable.
>> >> I assume you got plenty of that.
>> >>
>> >> On linux I would then use 'strace' to see if the kernel tells me more.
>> >> And the ldd
>> >> command to see what shared libs it might need.
>> >>
>> >> On a mac, there appears to be the dtruss command for strace. Me and Mac
>> >> appear
>> >> to be in a continues state of dislike, all I got was
>> >>    dtrace: failed to initialize dtrace: DTrace requires additional
>> >> privileges
>> >> so I'm sure somebody can tell me what that means (I don't have admin on
>> >> that mac)
>> >>
>> >> peter
>> >>
>> >>
>> >> On 09/28/2014 03:36 PM, Mordecai-Mark Mac Low wrote:
>> >>> Hi, I am having a fatal problem installing yt on my MacBook Pro
>> >>> running OS X v10.9.4.  I am using the install script, with the options
>> >>> set as follows:
>> >>>
>> >>>
>> >>> # Here's where you put the HDF5 path if you like; otherwise it'll
>> >>> download it
>> >>> # and install it on its own
>> >>> #HDF5_DIR=/opt/local/lib
>> >>>
>> >>> # If you need to supply arguments to the NumPy or SciPy build, supply
>> >>> them here
>> >>> # This one turns on gfortran manually:
>> >>> #NUMPY_ARGS="--fcompiler=gnu95"
>> >>> # If you absolutely can't get the fortran to work, try this:
>> >>> #NUMPY_ARGS="--fcompiler=fake"
>> >>>
>> >>> INST_HG=0       # Install Mercurial or not?  If hg is not already
>> >>>                # installed, yt cannot be installed.
>> >>> INST_ZLIB=1     # On some systems (Kraken) matplotlib has issues with
>> >>>                # the system zlib, which is compiled statically.
>> >>>                # If need be, you can turn this off.
>> >>> INST_BZLIB=1    # On some systems, libbzip2 is missing.  This can
>> >>>                # lead to broken mercurial installations.
>> >>> INST_PNG=1      # Install a local libpng?  Same things apply as with
>> >> zlib.
>> >>> INST_FTYPE=1    # Install FreeType2 locally?
>> >>> INST_ENZO=0     # Clone a copy of Enzo?
>> >>> INST_SQLITE3=1  # Install a local version of SQLite3?
>> >>> INST_PYX=1      # Install PyX?  Sometimes PyX can be problematic without
>> >> a
>> >>>                # working TeX installation.
>> >>> INST_0MQ=1      # Install 0mq (for IPython) and affiliated bindings?
>> >>> INST_ROCKSTAR=1 # Install the Rockstar halo finder?
>> >>> INST_SCIPY=0    # Install scipy?
>> >>>
>> >>>
>> >>> After downloading and activating Xcode command line tools, I got the
>> >>> script to complete successfully. I activated it using the activate.csh
>> >>> script.
>> >>>
>> >>> However, when I then try to start yt, it pauses for 30 seconds or so,
>> >>> and then issues the response ?Abort?, with no further errors.  I get
>> >>> the same response if I try to import yt into the python (running in
>> >>> the yt environment). Abort, and return to the command line.
>> >>>
>> >>> I have tried erasing the yt-x86_64 directory and reinstalling from
>> >>> scratch, with no change in behavior.  I also examined the
>> >>> yt_install.log.  I found a number of, presumably irrelevant, errors in
>> >>> the configuration tests, but also an error at the end of the long
>> >>> section on building Ipython (almost at the end of the script, just
>> >>> before readline assembly that looks possibly relevant:
>> >>>
>> >>>    gcc -dynamic -arch i386 -arch x86_64 -arch_only `/usr/bin/arch`
>> >>> -install_name /usr/local/lib/libreadline.6.2.dylib -current_version
>> >>> 6.2 -compatibility_version 6 -v -o libreadline.6.2.dylib readline.so
>> >>> vi_mode.so funmap.so keymaps.so parens.so search.so rltty.so
>> >>> complete.so bind.so isearch.so display.so signals.so util.so kill.so
>> >>> undo.so macro.so input.so callback.so terminal.so text.so nls.so
>> >>> misc.so xmalloc.so xfree.so history.so histexpand.so histfile.so
>> >>> histsearch.so shell.so mbutil.so tilde.so compat.so -lncurses
>> >>>    Apple LLVM version 6.0 (clang-600.0.51) (based on LLVM 3.5svn)
>> >>>    Target: x86_64-apple-darwin13.3.0
>> >>>    Thread model: posix
>> >>>    clang: error: invalid argument '-compatibility_version 6' only
>> >>> allowed with '-dynamiclib'
>> >>>    clang: error: invalid argument '-compatibility_version 6' only
>> >>> allowed with '-dynamiclib'
>> >>>    make[1]: *** [libreadline.6.2.dylib] Error 1
>> >>>    make: [shared] Error 2 (ignored)
>> >>>
>> >>> Any insight on how to proceed?
>> >>>
>> >>> Best,
>> >>>
>> >>> Mordecai
>> >>>
>> >>>
>> >>> --
>> >>> Mordecai-Mark Mac Low Curator & Professor
>> >>> +1-212-496-3443         Department of Astrophysics
>> >>> +1-212-769-5007 (fax)   American Museum of Natural History
>> >>> mmaclow (Skype, Hangout)    79th St at CPW, NY, NY, 10024-5192, USA
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
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>> 
>> --
>> Mordecai-Mark Mac Low           Curator & Professor
>> +1-212-496-3443                Department of Astrophysics
>> +1-212-769-5007 (fax)          American Museum of Natural History
>> mmaclow (Skype, Hangout)        79th St at CPW, NY, NY, 10024-5192, USA
>> 
>> 
>> 
>> 
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> 
>> 
> 
> 
> --
> Mordecai-Mark Mac Low 		Curator & Professor
> +1-212-496-3443         	Department of Astrophysics
> +1-212-769-5007 (fax)   	American Museum of Natural History
> mmaclow (Skype, Hangout)    	79th St at CPW, NY, NY, 10024-5192, USA
> 
> 
> 
> 
> 

--
Mordecai-Mark Mac Low 		Curator & Professor
+1-212-496-3443         	Department of Astrophysics
+1-212-769-5007 (fax)   	American Museum of Natural History
mmaclow (Skype, Hangout)    	79th St at CPW, NY, NY, 10024-5192, USA




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